Lorena Escudero

Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)

Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO2 fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.

Distribution of prokaryotic genetic diversity in athalassohaline lakes of the Atacama Desert, Northern Chile

Athalassohaline lakes are inland saline aquatic environments with ionic proportions quite different from the dissolved salts in seawater. Prokaryotes inhabiting athalassohaline environments are poorly known and very few of such places have been surveyed for microbial diversity studies around the world. We analyzed the planktonic bacterial and archaeal assemblages inhabiting several of these evaporitic basins in a remote and vast area in northern Chile by PCR-denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene fragments. Most systems were springs and athalassohaline ponds in different saltflats of the Atacama Desert region, including Salar de Llamará (in the Central Depression), Salar de Atacama (in the Pre-Andean Depression) and Salar de Ascotán (in the Altiplano). Overall, we analyzed more than 25 samples from 19 different environments with strong gradients of altitude, qualitative ionic compositions and UV influence. Between 4 and 25 well-defined DGGE bands were detected for Bacteria in each sample, whereas Archaea ranged between 1 and 5. Predominant DGGE bands (defined by intensity and frequency of appearance) were excised from the gel and sequenced. Bacterial assemblages were dominated by the Cytophaga-Flavobacterium-Bacteroides (CFB) phylum and a few Proteobacteria. There was a tendency for increasing contribution of CFB with higher salinities and altitude. Thus, CFB accounted for the major fraction of band intensity in the Ascotán samples and for lower percentages in Atacama and Llamará. When the distribution of particular CFB sequences was examined, there were several relatives of Psychroflexus torquis substituting each other as salinity changed in Ascotán. Another set of CFB sequences, very distantly related to Cytophaga marinovorus, was abundant in both Llamará and Atacama at salinities lower than 7%. Archaeal assemblages were dominated by uncultured haloarchaea distantly related to cultured strains mostly obtained from thalassohaline environments. Most of the archaeal sequences did not have a close match with environmental 16S rRNA genes deposited in the database either. Therefore, athalassohaline environments are excellent sources of new microorganisms different from their counterparts in thalassohaline sites and useful tools to relate microbial genetic diversity and environmental characteristics such as changes in salinity (both qualitative and quantitative) and altitude.

Tapetes microbianos del Salar de Llamará, norte de Chile

Stratified photosynthetic microbial mats are described from the Salar de Llamara, a salt flat basin located in the Atacama desert of northern Chile. Microscopic and spectrophotometric techniques were used. The thickness of the photic zone of these communities spans 8 to 30 mm. This is probably due to the grain size and mineralogical composition of associated sediments. Three different types of mats were recognized. A first one was characterized by a green pigmented layer; a second with orange and green coloured layers, and the third with orange and green layers and an additional purple layer. At one sampling site, no pigmented layers were present. Sediments underlying the mats were white, but in one site, black coloured sediments were observed; this dark colour is probably the result of iron sulphide precipitation. Predominant microorganisms in the orange pigmented layers were diatoms and unicellular cyanobacteria, mainly from the Cyanothece and Synechococcus groups. Filamentous cyanobacteria Microleus sp. and Oscillatoria sp. were the most abundant in the green layer. When interstitial brines reached salinities between 12 and 33 %, no diatoms were observed, and the coccoidal cyanobacteria from the Synechococcus, Cyanothece and Gloeocapsa groups and genus Gloeobacter predominated over filamentous Cyanobacteria in the green layer. The purple layer was built primarily of anoxygenic phototrophic bacteria similar to cells of the genera Chromatium and Thiocapsa. Absorption spectra revealed that chlorophyll a is the most abundant pigment in most of analyzed samples. Integrated values of chlorophyll a and bacteriochlorophyll a reached values of up to 230 and 144 mg m -2 along all of the pigmented zone, respectively. Abundant non-photosynthetic microorganisms were found in the mats, including unidentified cocci and bacilli. Sulphate reducing bacteria were present in all the sampled mats.

Distribution of Microbial Arsenic Reduction, Oxidation and Extrusion Genes along a Wide Range of Environmental Arsenic Concentrations

The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V) as electron acceptor, was found in all the systems studied. The As (III) oxidation gene aioA and the As (III) transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx)-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations.

Investigating microbial diversity and UV radiation impact at the high-altitude Lake Aguas Calientes, Chile

The High-Lakes Project is funded by the NAI and explores the highest perennial volcanic lakes on Earth in the Bolivian and Chilean Andes, including several lakes ~6,000 m elevation. These lakes represent an opportunity to study the evolution of microbial organisms in relatively shallow waters not providing substantial protection against UV radiation. Aguas Calientes (5,870 m) was investigated (November 2006) and samples of water and sediment collected at 1, 3, 5, and 10 cm depth. An Eldonet UV dosimeter positioned on the shore records UV radiation and temperature, and is logging data year round. A UV SolarLight sensor allowed acquisition of point measurements in all channels at the time of the sampling. UVA, UVB, and PAR peaks between 11:00 am and 1:00 pm reached 7.7 mW/cm2, 48.5 μW/cm2, and 511 W/m2, respectively. The chemical composition of the water sample was analyzed. DNA was extracted and DGGE analyses with bacterial and archaeal 16S fragments were performed to describe microbial diversity. Antibiotic resistances were established previously in similar environments in Argentine Andean wetlands. In order to determine these resistances in our samples, they were inoculated onto LB and R2A media and onto R2A medium containing either chloramphenicol, ampicillin or tetracycline. Bacterial was higher than archeal cell number determined by RT-PCR in all the samples, reaching maximum total values of 5x105 cell mL-1. DGGE results from these samples and Licancabur summit lake (5,916 m) samples were also compared. Eight antibiotic-resistant Gram negative strains have been isolated with distinct resistance patterns.

Signatures of Habitats and Life in Earth’s High-Altitude Lakes: Clues to Noachian Aqueous Environments on Mars

14.1 IntroductionA series of astrobiological high-altitude expeditions to the South AmericanAndean Mountains were initiated in 2002 to explore the highest perenniallakes on Earth, including several volcanic crater lakes at or above 6000 min elevation. During the next five years, they will provide the first integratedlong-term astrobiological characterization and monitoring of lacustrineenvironments and their biology at such an altitude. These extreme lakesare natural laboratories that provide the field data, currently missingabove 4000 m, to complete our understanding of terrestrial lakes and biota.Research is being performed on the effects of UV in low-altitude lakesand models of UV flux over time have been developed (Cockell, 2000). Thelakes showing a high content of dissolved organic material (DOM) shieldorganisms from UV effects (McKenzie et al., 1999; Rae et al., 2000). DOMacts as a natural sunscreen by influencing water transparency, and thereforeis a determinant of photic zone depth (Reche et al., 2000). In sparselyvegetated alpine areas, lakes tend to be clearer and offer less protectionfrom UV to organisms living in the water. Transparent water, combinedwith high UV irradiance may maximize the penetration and effect of UVradiation as shown for organisms in alpine lakes (e.g., Vincent et al., 1984;Vinebrook and Leavitt, 1996). Shallow-water benthic communities in theselakes are particularly sensitive to UV radiation. Periphyton, which definescommunities of microorganisms in bodies of water, can live on varioussusbtrates. While on rocks, they include immobile species that cannot seeklow UV refuges unlike sediment-dwelling periphyton (Happey-Wood, 1988;Vincent et al., 1993) or alpine phytoflagellates (Rott, 1988) which bothundergo vertical migration. Inhibition of algal photosynthesis by UV radia-tion has been documented in the laboratory (Ha ¬der, 1993) and it has beenshown that phytoplankton production is reduced by formation of nucleic acidlesions (Karentz et al., 1991) or production of peroxides and free oxygenradicals (Cooper et al., 1989). Most of the experiments that have demon-strated in situ suppression of algal growth by UV radiation have eitherused artificially enhanced UV irradiance (Worrest et al., 1978) or shallowsystems (<1 cm) that lack significant natural attenuation of UV radiation(Bothwell et al., 1993, 1994). Our project is providing the field data thatare missing from natural laboratories above 4000 m and will complementthe postulation of the effects of UV on life and its adaptation modes(or lack thereof).The exploration of high-altitude lakes could shed light on early EarthOsbiological evolution as well. For two billion years, EarthOs atmosphere

Draft Genome Sequence of Nitrincola sp. Strain A-D6, an Arsenic-Resistant Gammaproteobacterium Isolated from a Salt Flat.

ABSTRACT We report Nitrincola sp. strain A-D6, which was characterized as an arsenic-resistant bacterium isolated from the Ascotán Salt Flat in northern Chile. The size of the genome is 3,795,776 bp, with a G+C content of 49.96%. Genes for the arsenic-resistant Ars system and arsenic oxidation have been encoded.

The ecological coherence of temperature and salinity tolerance interaction and pigmentation in a non-marine vibrio isolated from Salar de Atacama

The occurrence of microorganisms from the Vibrio genus in saline lakes from northern Chile had been evidenced using Numerical Taxonomy decades before and, more recently, by phylogenetic analyses of environmental samples and isolates. Most of the knowledge about this genus came from marine isolates and showed temperature and salinity to be integral agents in shaping the niche of the Vibrio populations. The stress tolerance phenotypes of Vibrio sp. Teb5a1 isolated from Salar de Atacama was investigated. It was able to grow without NaCl and tolerated up to 100 g/L of the salt. Furthermore, it grew between 17° and 49°C (optimum 30°C) in the absence of NaCl, and the range was expanded into cold temperature (4–49°C) in the presence of the salt. Other additional adaptive strategies were observed in response to the osmotic stress: pigment production, identified as the known antibacterial prodigiosin, swimming and swarming motility and synthesis of a polar flagellum. It is possible to infer that environmental congruence might explain the cellular phenotypes observed in Vibrio sp. considering that coupling between temperature and salinity tolerance, the production of antibacterial agents at higher temperatures, flagellation and motility increase the chance of Vibrio sp. to survive in salty environments with high daily temperature swings and UV radiation.

Geochemistry and Microbiology in an Acidic, High Altitude (4,000 m) Salt Flat — High Andes, Northern Chile

Acidic saline lake systems are an uncommon type of natural extreme environment described in Northern Chile and in Australia. These environments are considered a terrestrial analogue to certain ancient Martian terrains and a source of new material for biotechnological applications as bioleaching at high ionic strength conditions and biological systems for precipitating metal sulfides. The aim of this study is to describe the occurrence of redox couples that support prokaryotic life in the system and to obtain representative cultures of predominant microorganisms/metabolisms. Mapping of the area of interest and geochemical analysis of sediments, bedrock and water samples were performed. The original microbial community and enriched cultures were studied by direct count and culturing dependent and independent techniques. In the distal part of the alluvial fans some ponds are found with acidic brines (up to pH 1) of the Cl-SO4-Na (-Mg) type that are surrounded by yellow efflorescences. Other ponds towards the basin center progressively increase in concentration due to capillary evaporation. Brines are rich in aluminium and boron with lower concentration of manganese, lithium, iron and arsenic. An advanced hydrothermal argillic alteration affecting the country rocks, native sulfur associated to active solfataras, alunite and jarosite occurrences in sediments and chloride and sulfate efflorescent salts were evidenced. The microbial community in brines and sediments (105 and 106 cells/mL, respectively) was dominated by Firmicutes, Proteobacteria and Actinobacteria, and by Proteobacteria and Cyanobacteria, respectively. Sulphur and iron oxidation activity were detected depending on the salinity of the samples. Culture enrichments that respire and reduce As (V) and sulfate have been only obtained from sites with the highest pH (4-5). Microbial assemblages in those heterotrophic cultures were closely related to the Gamma and Betaproteobacteria, meanwhile, Rhodanobacter and Shewanella were the only microorganisms detected in the autotrophic cultures supplemented by Na2S and by H2. Relevant information to describe the occurring surface biogeochemical processes in that acidic saline system has been obtained. In addition, the occurrence of new prokaryotic genera capable of arsenic redox transformation has been evidenced in acidic systems.

A thiotrophic microbial community in an acidic brine lake in Northern Chile

The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.